PDBe 5f8k

X-ray diffraction
2.8Å resolution

Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Cathelicidin-3 Chains: 1y, 2y
Molecule details ›
Chains: 1y, 2y
Length: 16 amino acids
Theoretical weight: 2.08 KDa
Source organism: Bos taurus
Expression system: Not provided
UniProt:
  • Canonical: P19661 (Residues: 131-146; Coverage: 10%)
Gene names: BAC7, CATHL3
30S ribosomal protein S2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 231 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-237; Coverage: 90%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 148 amino acids
Theoretical weight: 16.14 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-152; Coverage: 91%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 100 amino acids
Theoretical weight: 11.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-100; Coverage: 99%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
30S ribosomal protein S8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 2-138; Coverage: 99%)
Gene names: TTHA1678, rpsH
30S ribosomal protein S9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 127 amino acids
Theoretical weight: 14.28 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
50S ribosomal protein L2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-204; Coverage: 99%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
Length: 203 amino acids
Theoretical weight: 22.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-208; Coverage: 97%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 174 amino acids
Theoretical weight: 18.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0M9ADP1 (Residues: 2-175; Coverage: 97%)
Gene names: BVI061214_01035, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 147 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-147; Coverage: 99%)
Gene names: TTHA0242, rplI
Sequence domains:
30S ribosomal protein S10 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 97 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 4-100; Coverage: 92%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 114 amino acids
Theoretical weight: 12.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 13-126; Coverage: 88%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 122 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-123; Coverage: 92%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 116 amino acids
Theoretical weight: 13.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-117; Coverage: 92%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 82 amino acids
Theoretical weight: 9.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-82; Coverage: 93%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 2-100; Coverage: 94%)
Gene names: TTHA1683, rpsQ
30S ribosomal protein S18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 68 amino acids
Theoretical weight: 7.9 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 20-87; Coverage: 77%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 83 amino acids
Theoretical weight: 9.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-84; Coverage: 89%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
Length: 98 amino acids
Theoretical weight: 10.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 6-103; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 23 amino acids
Theoretical weight: 2.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-24; Coverage: 85%)
Gene names: TTHA1396, rpsU
50S ribosomal protein L13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 149 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-149; Coverage: 99%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 110 amino acids
Theoretical weight: 12.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 3-112; Coverage: 98%)
Gene names: TTHA1676, rplR
50S ribosomal protein L19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
Length: 131 amino acids
Theoretical weight: 15.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-131; Coverage: 90%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-117; Coverage: 98%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-112; Coverage: 99%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 95 amino acids
Theoretical weight: 10.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-95; Coverage: 99%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 107 amino acids
Theoretical weight: 11.73 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-107; Coverage: 97%)
Gene names: TTHA1681, rplX
Sequence domains:
50S ribosomal protein L25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 203 amino acids
Theoretical weight: 22.85 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-203; Coverage: 99%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 8-84; Coverage: 91%)
Gene names: TTHA1782, rpmA
50S ribosomal protein L28 Chains: 11, 21
Molecule details ›
Chains: 11, 21
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 2-98; Coverage: 99%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 70 amino acids
Theoretical weight: 8.49 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-70; Coverage: 97%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-69; Coverage: 97%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 53 amino acids
Theoretical weight: 6.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 2-54; Coverage: 98%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-65; Coverage: 99%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
30S ribosomal protein S14 type Z Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 2-61; Coverage: 98%)
Gene names: TTHA1679, rpsN, rpsZ
tRNAiMet Chains: 1x, 2x
Molecule details ›
Chains: 1x, 2x
Length: 76 nucleotides
Theoretical weight: 24.54 KDa
Sequence domains: tRNA
Messenger RNA Chains: 1v, 2v
Molecule details ›
Chains: 1v, 2v
Length: 3 nucleotides
Theoretical weight: 936 Da
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 1520 nucleotides
Theoretical weight: 493.56 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 948.01 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P212121
Unit cell:
a: 209.96Å b: 450.13Å c: 622.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.249 0.292
Expression system: Not provided